[BioC] Reading Agilent files using read.maimages

[Misha Kapushesky]

Dear Steve et al,

The files you downloaded from ArrayExpress are in fact in its own  
format. For this experiment, in case you might find it useful, we  
placed the original Agilent raw data files as given to us by the  
submitter at ftp://ftp.ebi.ac.uk/pub/databases/microarray/data/ 
experiment/MEXP/E-MEXP-668/E-MEXP-668.original-raw-data.tar.gz.

Hope this helps.

--Misha K.
Microarray Informatics Team, EBI

On 16 Aug 2007, at 14:35, Steve Taylor wrote:

> Hi,
>
> I removed the prefixes from the file headers and they eventually  
> read in.
>
> I did get:
>
> Read ./E-MEXP-668-raw-data-921408043.txt
> Read ./E-MEXP-668-raw-data-921408048.txt
> Read ./E-MEXP-668-raw-data-921408053.txt
> Read ./E-MEXP-668-raw-data-921408058.txt
> Error in RG[[a]][, i] <- obj[, columns[[a]]] :
>          number of items to replace is not a multiple of  
> replacement length
>
> which I think is due to inconsistent numbers of columns in some  
> files (and read.maimages doesn't seem to cope with), but I managed  
> to get round this by reording the targets file. I have got the data
> to normalise now.
>
> Thank you all very much for helping me on this problem.
>
> Steve
>
>
>> I have download the files and it seems that each file has its own
>> header. By this I mean that a prefix has been add to each standard  
>> column.
>> For example, for file "E-MEXP-668-raw-data-921408043.txt" every  
>> column
>> start with "H_C1 A_mock A and B/" whereas in file
>> "E-MEXP-668-raw-data-921408128.txt" it is "H_C52 B_mock A and B/". In
>> order to make the read.maimages work you should remove those  
>> prefixes. I
>> have changed it for a couple of slides and it worked for me.
>>
>> targets <-read.("AE.csv", path=".",sep=",")
>> RG <- read.maimages(targets$FileName[c 
>> (1,16)]),path=".",source="agilent")
>> Read ./E-MEXP-668-raw-data-921408043.txt
>> Read ./E-MEXP-668-raw-data-921408118.txt
>>
>>> str(RG$G)
>>
>>  num [1:22153, 1:2] 960.4  73.1  83.3 648.1 132.9 ...
>>  - attr(*, "dimnames")=List of 2
>>   ..$ : NULL
>>   ..$ : chr [1:2] "E-MEXP-668-raw-data-921408043"
>> "E-MEXP-668-raw-data-921408118"
>>
>> Hope it helps,
>> Nolwenn
>>
>> Scott Reagan Franklin wrote:
>>
>>> Steve:
>>>
>>> It should be noted that when you are using read.maimages with
>>> source="agilent" and you are using the actual Agilent Raw Data file,
>>> you will, by default, have RG$R and RG$G equal to the rMeanSignal  
>>> and
>>> gMeanSignal.  In order to specify that they be equal to the
>>> rProcessedSignal and gProcessedSignal you need to add an option to
>>> read.maimages:
>>>
>>> RG<-read.maimages(targets$FileName,path=".",columns=list 
>>> (R="rProcessedSignal",G="gProcessedSignal));
>>>
>>> You can also specify which background signal is used as well by
>>> including in Rb and Gb in the list above.  By default Rb and Gb are
>>> chosen as the median background signals.
>>>
>>>
>>>
>>
>
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